Global alignment of molecular sequences via ancestral state reconstruction

Alexandr Andoni, Constantinos Daskalakis, Avinatan Hassidim, Sebastien Roch

Research output: Contribution to journalArticlepeer-review


We consider the trace reconstruction problem on a tree (TRPT): a binary sequence is broadcast through a tree channel where we allow substitutions, deletions, and insertions; we seek to reconstruct the original sequence from the sequences received at the leaves. The TRPT is motivated by the multiple sequence alignment problem in computational biology. We give a simple recursive procedure giving strong reconstruction guarantees at low mutation rates. To our knowledge, this is the first rigorous trace reconstruction result on a tree in the presence of indels.

Original languageEnglish
Pages (from-to)3852-3874
Number of pages23
JournalStochastic Processes and their Applications
Issue number12
StatePublished - Dec 2012


  • Branching processes
  • Markov models on trees
  • Phylogenetic inference

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Modelling and Simulation
  • Applied Mathematics


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